Pseudomonas Genome Database
Preview The Pseudomonas Genome database consists of over 40 complete, annotated genome sequences encompassing representative members of the Pseudomonas ''genus. The site is funded by the non-profit Cystic Fibrosis Foundation Therapeutics Inc., and is continuously updated using recently published literature and peer-reviewed submssions. History The ''Pseudomonas ''database was founded early in 2001, a year after the PA01 genome was sequenced and published in Nature. Funding for the start-up and development of the site was provided by The Cystic Fibrosis Foundation Inc. The page is currently maintained under the coordination of Fiona Brinkman, Ph.D., at Simon Fraser University and Robert Hancock, Ph.D., at the University of British Columbia, with database improvement and development led by Geoff Winsor of the Brinkman Group 1. Use of the database in primary research The Pseudomonas'' Genome Database is heavily utilized by researchers and has been cited over 40 times in PubMed this year alone. In one interesting study, Perumal et. al, used the database to compare the diversity in multiple metabolic pathways among the sequenced genomes of eight different pseudomonads. In doing so, they were able to reveal 11 instances where enzymes from different pathways were missing from the genome, and compensated for by the aquisition of different enzymes or regulatory mechanisms to bridge the loss of function within the pathway 2. Utility The database allows for inter and intragenomic comparisons through a browsing format utilizing NCBI-BLAST; letting users upload and search sequences both withi the Pseudomonas and NCBI databases at the nucleotide or amino acid levels. Additionally, the GBrowse function allows users to navigate the genome by viewing specific regulons and pathways at the operon level. Users can than zoom in to view the nucleotide sequence or zoom out to view the operon's location within the chromosome. In many cases, putative genes that have yet to be studied have predicted functions listed along with any conserved motifs or domains the speculative protein contains. How to search the database Searches can be performed by locus or gene/protein directly from the home page using the "Quick Search" box. An example of how to perform a search by gene name is shown below using Sarcosine Oxidase. 1) Select a genome of interest to search from the drop-down menu. 2) Select "Gene & Protein Names" from drop-down menu 3) Enter Sarcosine Oxidase in the search box 4) Click on the locus link to view the annotated soxB ''gene within the Sarcosine Oxidase Operon 5) Users can then view gene information using the tabs below, including the enzyme’s predicted function, DNA sequence, and it's predicted operon. References 1 Winsor GL, Lam DK, Fleming L, Lo R, Whiteside MD, Yu NY, Hancock RE, Brinkman FS (2011). Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res. 2011 Jan;39(Database issue):D596-600Perumal D, Lim CS, Chow VTK, Sakharkar KR, Sakharkar MK. 2 Perumal D, Lim CS, Chow VTK, Sakharkar KR, Sakharkar MK. A combined computational-experimental analyses of selected metabolic enzymes in ''Pseudomonas species. Int J Biol Sci 2008; 4(5):309-317. doi:10.7150/ijbs.4.309.